Proteins are composed of a series of amino acid residues. There are 20 naturally occurring amino acids. The three-dimensional structure of a protein typically comprises a series of folded regions. When profiling a protein, researchers attempt to determine the amino acid spatial order and location in three-dimensional space. The profiling of a protein is important because many of the functions associated with the human body depend on the particular protein structure.
Many proteins are globular and form in an aqueous environment. These globular proteins comprise hydrophobic amino acids that repel water, and hydrophilic amino acids that are attracted to water. When these proteins fold up, the hydrophobic amino acids are predominantly arranged in the non-aqueous center of the protein molecule and the hydrophilic amino acids are arranged on the aqueous protein surface. A protein formed in this manner will have a hydrophobic core and a hydrophilic exterior.
Of use in the study of protein structure is the ability to compare different structures. Decoy proteins have been developed to test the effectiveness of structure analysis methods. Decoy proteins are man-made protein structures that may be derived from naturally occurring proteins, but possess structural deviations. Decoy proteins can be used to test the sensitivity and effectiveness of structure analysis methods. For example, decoy proteins may be disbursed within a test set of proteins and the effectiveness of the analysis will be reflected by the identification of all the decoy proteins. Some commonly used protein decoys include the Holm & Sander decoys, the Park & Levitt decoys and the Baker decoys. A single native, i.e., naturally occurring, protein may be used to generate numerous decoy proteins. Therefore, any given set may comprise thousands of decoy proteins.
Accordingly, given such a large number of protein structures, effective techniques for comparing such protein structures would be desirable. Further, it would be desirable if such comparison could be performed for a plurality of structures.